Atomistry » Iron » PDB 6o6m-6op1 » 6of5
Atomistry »
  Iron »
    PDB 6o6m-6op1 »
      6of5 »

Iron in PDB 6of5: The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

Enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

All present enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase:
3.1.3.2;

Protein crystallography data

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5 was solved by D.Feder, G.Schenk, L.W.Guddat, W.M.Hussein, R.P.Mcgeary, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.808, 126.808, 298.211, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 23.1

Other elements in 6of5:

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6of5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 1 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:30.9
occ:0.66
 OAC A:MFJ528 1.8 33.5 0.7
OH A:TYR167 2.0 30.9 1.0
OD2 A:ASP135 2.0 28.0 1.0
OD2 A:ASP164 2.4 25.9 1.0
NE2 A:HIS325 2.5 31.5 1.0
OAD A:MFJ528 2.9 37.2 0.7
PBH A:MFJ528 2.9 35.5 0.7
CG A:ASP135 3.0 26.7 1.0
CZ A:TYR167 3.2 30.6 1.0
CG A:ASP164 3.3 26.4 1.0
ZN A:ZN501 3.3 28.2 0.8
CB A:ASP135 3.4 21.8 1.0
CD2 A:HIS325 3.4 28.8 1.0
CE1 A:HIS325 3.5 31.9 1.0
CB A:ASP164 3.6 26.2 1.0
OAB A:MFJ528 3.7 42.1 0.7
CE2 A:TYR167 3.8 27.5 1.0
OD1 A:ASP135 4.1 25.0 1.0
O A:HIS323 4.2 25.6 1.0
CD2 A:HIS202 4.2 33.4 1.0
CE1 A:TYR167 4.2 25.7 1.0
CBG A:MFJ528 4.3 43.1 0.7
OBC A:MFJ528 4.4 44.2 0.7
CA A:HIS323 4.4 29.1 1.0
OD1 A:ASP164 4.4 24.7 1.0
CA A:ASP135 4.4 25.0 1.0
CE1 A:HIS286 4.5 24.2 1.0
NE2 A:HIS286 4.6 22.1 1.0
CG A:HIS325 4.6 31.6 1.0
ND1 A:HIS325 4.6 34.1 1.0
NE2 A:HIS202 4.6 31.2 1.0
C A:HIS323 4.7 35.0 1.0
N A:HIS323 4.7 29.6 1.0
ND1 A:HIS323 4.9 34.9 1.0
OD1 A:ASN201 5.0 31.1 1.0

Iron binding site 2 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 2 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:38.5
occ:0.79
 OH B:TYR167 2.0 33.1 1.0
OD1 B:ASP135 2.0 30.6 1.0
OD2 B:ASP164 2.4 33.4 1.0
NE2 B:HIS325 2.5 34.1 1.0
CG B:ASP135 3.1 33.8 1.0
CZ B:TYR167 3.1 29.2 1.0
CD2 B:HIS325 3.4 32.3 1.0
ZN B:ZN501 3.4 39.5 1.0
CG B:ASP164 3.4 34.7 1.0
CE1 B:HIS325 3.5 27.2 1.0
CE2 B:TYR167 3.7 27.9 1.0
CB B:ASP135 3.7 31.2 1.0
CB B:ASP164 3.7 25.9 1.0
O B:HIS323 4.0 38.2 1.0
CD2 B:HIS202 4.1 33.1 1.0
OD2 B:ASP135 4.2 29.9 1.0
CE1 B:TYR167 4.2 30.7 1.0
NE2 B:HIS202 4.3 36.3 1.0
CA B:HIS323 4.4 32.3 1.0
OD1 B:ASP164 4.5 33.9 1.0
C B:HIS323 4.6 33.8 1.0
CG B:HIS325 4.6 34.9 1.0
ND1 B:HIS325 4.6 35.7 1.0
CA B:ASP135 4.6 31.6 1.0
NE2 B:HIS286 4.6 34.9 1.0
CE1 B:HIS286 4.7 27.2 1.0
N B:HIS323 4.8 35.4 1.0
OD1 B:ASN201 4.9 36.6 1.0
ND1 B:HIS323 4.9 33.8 1.0

Iron binding site 3 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 3 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:46.5
occ:0.72
 OD2 D:ASP135 1.9 32.5 1.0
OH D:TYR167 2.0 29.2 1.0
OD2 D:ASP164 2.6 33.2 1.0
NE2 D:HIS325 2.6 33.1 1.0
CG D:ASP135 3.1 35.1 1.0
CZ D:TYR167 3.1 32.8 1.0
ZN D:ZN501 3.3 35.9 0.9
CD2 D:HIS325 3.4 34.3 1.0
CG D:ASP164 3.6 33.6 1.0
CE2 D:TYR167 3.6 33.9 1.0
CE1 D:HIS325 3.7 32.2 1.0
CB D:ASP135 3.7 26.9 1.0
CB D:ASP164 3.9 31.8 1.0
O D:HIS323 3.9 34.1 1.0
OD1 D:ASP135 4.1 32.4 1.0
CD2 D:HIS202 4.2 29.3 1.0
CE1 D:TYR167 4.3 27.5 1.0
CA D:HIS323 4.3 29.5 1.0
C D:HIS323 4.5 32.1 1.0
NE2 D:HIS286 4.6 28.4 1.0
NE2 D:HIS202 4.6 32.4 1.0
CE1 D:HIS286 4.6 27.9 1.0
CA D:ASP135 4.6 25.7 1.0
CG D:HIS325 4.6 36.5 1.0
OD1 D:ASN201 4.7 36.8 1.0
OD1 D:ASP164 4.7 31.3 1.0
ND1 D:HIS325 4.7 34.5 1.0
ND1 D:HIS323 4.8 34.0 1.0
N D:HIS323 4.8 30.5 1.0

Iron binding site 4 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 4 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:40.4
occ:0.74
 OH C:TYR167 2.0 30.6 1.0
OD2 C:ASP135 2.0 35.7 1.0
OD2 C:ASP164 2.2 32.5 1.0
NE2 C:HIS325 2.6 35.9 1.0
CG C:ASP135 3.1 31.5 1.0
CZ C:TYR167 3.2 32.3 1.0
CG C:ASP164 3.2 35.0 1.0
ZN C:ZN501 3.4 31.4 0.9
CD2 C:HIS325 3.5 34.4 1.0
CB C:ASP135 3.5 27.4 1.0
CB C:ASP164 3.7 29.1 1.0
CE1 C:HIS325 3.7 36.3 1.0
CE2 C:TYR167 3.7 33.1 1.0
O C:HIS323 3.8 26.4 1.0
OD1 C:ASP135 4.1 34.1 1.0
CA C:HIS323 4.2 26.2 1.0
CE1 C:TYR167 4.3 30.2 1.0
OD1 C:ASP164 4.3 32.1 1.0
CD2 C:HIS202 4.4 31.4 1.0
C C:HIS323 4.4 30.3 1.0
CE1 C:HIS286 4.5 26.0 1.0
NE2 C:HIS286 4.5 30.9 1.0
CA C:ASP135 4.6 29.0 1.0
CG C:HIS325 4.7 35.3 1.0
N C:HIS323 4.7 27.9 1.0
NE2 C:HIS202 4.7 33.5 1.0
ND1 C:HIS325 4.7 37.8 1.0
OD1 C:ASN201 4.8 35.7 1.0
ND1 C:HIS323 4.9 29.2 1.0

Reference:

D.Feder, M.W.Kan, W.M.Hussein, L.W.Guddat, G.Schenk, R.P.Mcgeary. Synthesis, Evaluation and Structural Investigations of Potent Purple Acid Phosphatase Inhibitors As Drug Leads For Osteoporosis. Eur.J.Med.Chem. V. 182 11611 2019.
ISSN: ISSN 0223-5234
PubMed: 31445230
DOI: 10.1016/J.EJMECH.2019.111611
Page generated: Wed Aug 7 04:20:57 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy